knitr document van Steensel lab

TF reporter oligo design

Introduction

In this document, an oligo library of TF reporters will be generated. These oligos contain TF binding sites of ~30 selected TFs, random inactive spacing between them, followed by minimal promoters, and a barcode in the transcription unit.

Data processing

Path, Libraries, Parameters and Useful Functions

Custom functions

Functions used thoughout this script.

Data import

Analysis

Motif filtering and characterization

Session Info

paste("Run time: ",format(Sys.time()-StartTime))
## [1] "Run time:  12.37792 secs"
getwd()
## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/library_design/gen-2"
date()
## [1] "Thu Nov  5 10:45:01 2020"
sessionInfo()
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] stats4    parallel  grid      stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] ggrepel_0.8.1               ggbeeswarm_0.6.0           
##  [3] vwr_0.3.0                   latticeExtra_0.6-29        
##  [5] lattice_0.20-38             stringdist_0.9.5.5         
##  [7] data.table_1.12.8           RColorBrewer_1.1-2         
##  [9] ggseqlogo_0.1               tibble_3.0.1               
## [11] pheatmap_1.0.12             heatmaply_1.0.0            
## [13] viridis_0.5.1               viridisLite_0.3.0          
## [15] plotly_4.9.2.1              tidyr_1.0.0                
## [17] stringr_1.4.0               readr_1.3.1                
## [19] dplyr_0.8.5                 magrittr_1.5               
## [21] phylotools_0.2.2            ape_5.4-1                  
## [23] DNABarcodes_1.14.0          Matrix_1.2-18              
## [25] gtools_3.8.1                SimRAD_0.96                
## [27] zlibbioc_1.30.0             ShortRead_1.42.0           
## [29] GenomicAlignments_1.20.1    SummarizedExperiment_1.14.1
## [31] DelayedArray_0.10.0         matrixStats_0.55.0         
## [33] Biobase_2.44.0              Rsamtools_2.0.3            
## [35] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0        
## [37] BiocParallel_1.18.1         Biostrings_2.52.0          
## [39] XVector_0.24.0              IRanges_2.18.3             
## [41] S4Vectors_0.22.1            BiocGenerics_0.30.0        
## [43] universalmotif_1.2.1        seqLogo_1.50.0             
## [45] seqinr_3.6-1                ggplot2_3.3.0              
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_1.4-1       ggtree_1.16.6          hwriter_1.3.2         
##  [4] ellipsis_0.3.0         farver_2.0.1           codetools_0.2-16      
##  [7] knitr_1.30             ade4_1.7-13            jsonlite_1.7.1        
## [10] cluster_2.1.0          png_0.1-7              shiny_1.4.0           
## [13] BiocManager_1.30.10    compiler_3.6.3         httr_1.4.1            
## [16] rvcheck_0.1.7          fastmap_1.0.1          assertthat_0.2.1      
## [19] lazyeval_0.2.2         later_1.1.0.1          htmltools_0.5.0       
## [22] tools_3.6.3            gtable_0.3.0           glue_1.4.2            
## [25] GenomeInfoDbData_1.2.1 Rcpp_1.0.5             vctrs_0.2.4           
## [28] gdata_2.18.0           nlme_3.1-143           crosstalk_1.0.0       
## [31] iterators_1.0.12       gbRd_0.4-11            xfun_0.19             
## [34] ps_1.3.0               mime_0.9               lifecycle_0.2.0       
## [37] dendextend_1.13.2      MASS_7.3-51.5          scales_1.1.0          
## [40] TSP_1.1-7              promises_1.1.1         hms_0.5.3             
## [43] yaml_2.2.1             gridExtra_2.3          stringi_1.5.3         
## [46] gclus_1.3.2            foreach_1.4.7          tidytree_0.3.1        
## [49] seriation_1.2-8        caTools_1.17.1.4       bibtex_0.4.2.2        
## [52] Rdpack_0.11-1          rlang_0.4.8            pkgconfig_2.0.3       
## [55] bitops_1.0-6           BH_1.72.0-3            evaluate_0.14         
## [58] purrr_0.3.3            labeling_0.3           treeio_1.8.2          
## [61] htmlwidgets_1.5.2      processx_3.4.1         tidyselect_1.1.0      
## [64] R6_2.5.0               gplots_3.0.3           pillar_1.4.3          
## [67] withr_2.1.2            RCurl_1.95-4.12        crayon_1.3.4          
## [70] KernSmooth_2.23-16     rmarkdown_2.5          jpeg_0.1-8.1          
## [73] digest_0.6.27          webshot_0.5.2          xtable_1.8-4          
## [76] httpuv_1.5.4           munsell_0.5.0          beeswarm_0.2.3        
## [79] registry_0.5-1         vipor_0.4.5